Issue with piping from pysradb search to pysradb download

saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

https://saketkc.github.io/pysradb

BSD 3-Clause "New" or "Revised" License

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Closed bscrow closed 3 years ago

bscrow commented 4 years ago

When I was trying to pipe the output from pysradb search to pysradb download, a FileNotFoundError was raised.

pysradb search -m 100 -q ribosome profiling --db ena -v 1 | pysradb download

saketkc commented 4 years ago

I just pushed https://github.com/bscrow/pysradb/commit/cffdd78d03aba8fd355f57301a5e3bf4cc498d8e to your fork. It is meant as a fix, but doesn't work yet. I was not able to get the downloads to work on ftp mode. Would you be willing to give it a shot?

saketkc commented 4 years ago

Any updates on this @bscrow?

bscrow commented 3 years ago

Fixed in #57 An working example can be found here: